DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria

Kenneth I Brewer; Glenn J Gaffield; Malavika Puri; Ronald R Breaker

doi:10.1093/bioinformatics/btab624

DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria

Bioinformatics. 2022 Jan 3;38(2):533-535. doi: 10.1093/bioinformatics/btab624.

Authors

Kenneth I Brewer¹, Glenn J Gaffield², Malavika Puri³, Ronald R Breaker^{1

2

3}

Affiliations

¹ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
² Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA.
³ Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.

Abstract

Summary: Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL (Discovery of Intergenic Motifs PipeLine) discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification.

Availability and implementation: The DIMPL pipeline is freely available as a Docker image with an accompanying set of Jupyter notebooks. Full instructions for download and use are available at https://github.com/breakerlab/dimpl.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Bacteria* / genetics
Computational Biology / methods
Nucleotide Motifs
RNA, Untranslated / genetics
Riboswitch*

Substances

Riboswitch
RNA, Untranslated

Abstract

Publication types

MeSH terms

Substances

Grants and funding